There is no pipeline for genome annotation, but there are many different tools which you can use to annotate your genome. Gene prediction, RNA prediction, Genome Assembly, Target prediction etc ... everything is available in the Galaxy TS. A small group of hackers has started to collect all these tools and we are writing on some tutorial / training material at the moment. I will keep you posted when we make progress.
For the time being have a look at our Docker flavour for Genome Annotation: https://github.com/bgruening/docker-galaxy-genome-annotation
Hope this gets you started!
P.S. If you are nearby Freiburg/Germany we will have a Galaxy Genome Annotation workshop in June.